RNA molecules are targets for small molecule drugs. In fact, several clinically useful drugs operate by interfering with RNA function. Perhaps the most noteworthy examples are found among the antibiotics, and here the most useful RNA binding drugs are the aminoglycosides (Gale, E. F., Cundliffe, E., Reynolds, P. E., Richmond, M. H., & Waring M. J. (1981) The Molecular Basis of Antibiotic Action, 2nd ed., John Wiley & Sons, London, Great Britain, pp 419-439; Cundliffe, E. (1989) Annu. Rev. Microbiol. 43, 207-233). Aminoglycoside antibiotics function by binding to the A-site decoding region on bacterial 16S ribosomal (r)RNA (Scheme 1/fig9) (Noller, H. F. (1991) Annu. Rev. Biochem. 60, 191-227; Woodcock, J., Moazed, D., Cannon, M., Davies, J. and Noller, H. F. (1991) EMBO J. 10, 3099-3103). This binding alters the interactions between the codon-anticodon helix and the A-site RNA, causing mis-translation, and premature termination during protein synthesis in bacteria. This leads to the bactericidal effects of this class of drugs (Cundliffe, E. (1990) The Ribosome: Structure, Function & Evolution (Hill, W. E., Dahlberg, A. E., Garret, R. A., Moore, P. B., Schlessinger, D., & Warner, J. R., Eds.), American Society for Microbiology, Washington, D.C., pp 479-490; Chambers, H. F., & Sande, M. A. (1996) Goodman & Gilman's The Pharmacological Basis of Therapeutics (Hardman, J. G., Limbird, L. E., Molinoff, P. B., Ruddon, R. W., & Gilman, A. G., Eds.) 9th ed., McGraw-Hill, New York. Chap. 46, pp 1103-1121). An essential question to address with aminoglycosides is how specific are their interactions with targets, and to what structural elements do they owe their specificity of action.
Aminoglycosides have been found to bind to many different types of RNA structures (Zapp, M. L., Stern, S., & Green, M. R. (1993) Cell 74, 969-978; Werstuck, G., Zapp., M. L., & Green, M. R. (1996) Chem. Biol. 3, 129-137; Mei, H. Y., Cui, M., Heldsinger, A., Lemrow, S. M., Loo, J. A., Sannes-Lowery, K. A., Sharmeen, L., and Czarnik, A. W. (1998) Biochemistry 37, 14204-14212; Tok, J. B., Cho, J., & Robert, R. R. (1999) Biochemistry 38, 199-206; Stage, T. K., Hertel. K. J., & Uhlenbeck, O. C. (1995) RNA 1, 95-101). In addition to their pharmacologically relevant A-site decoding region targets (Scheme 1/fig9), aminoglycosides have been found to bind to regions of HIV mRNA, to thymidylate synthase mRNA, and to a variety of RNA molecules selected to bind to aminoglycosides (Wang, Y., & Rando, R. R. (1995) Chem. Biol. 2, 281-290; Lato, S. M., Boles, A. R., & Ellington, A. D. (1995) Chem. Biol. 2, 291-303; Wallis, M. G., Von Asen, U., Schroeder, R., & Famulok, M. (1995) Chem. Biol. 2, 543-552). Save for one notable instance, in which nM binding is found (Cho, J., Hamasaki, K., and Rando, R. R. (1998) Biochemistry 37, 4985-4992;Hamasaki, K., Killian, J. Cho, J., and Rando, R. R. (1998) Biochemistry 37, 656-663), typical binding affinities in the μM range are found for the interactions of aminoglycosides and RNA molecules. RNA molecules that bind to aminoglycosides typically possess non-duplex structural elements (Cho, J. and Rando, R. R. (1999) Biochemistry 38, 8548-8554). Often these RNA molecules contain asymmetric bulges or bubbles, which allow aminoglycoside access to the purine and pyrimidine bases.
Previous binding experiments on prokaryotic A-site decoding region RNA constructs measured affinities for D-aminoglycosides in the 1-2 μM range, save for neomycin B, which had a somewhat higher affinity. Similar observations were also made in studies on the binding of D-aminoglycosides to human decoding region A-site constructs. Binding studies have established that a wide variety of structurally dissimilar D-aminoglycosides have similar affinities for RNA substrates. See, for example, Ryu, D. H. and Rando, R. R. Bioorganic and Medicinal Chemistry, (In Press); and Wang, Y., Hamasaki, K., & Rando, R. R. (1997) Biochemistry 36, 768-77.
A structurally diverse family of D-aminoglycosides are known to be effective antibiotics (Chambers, H. F., & Sande, M. A. (1996) Goodman & Gilman's The Pharmacological Basis of Therapeutics (Hardman, J. G., Limbird, L. E., Molinoff, P. B., Ruddon, R. W., & Gilman, A. G., Eds.) 9 th ed., McGraw-Hill, New York. Chap. 46, pp 1103-1121).
The ready development of resistant strains of various organisms to aminoglycoside compounds limits the application of these compounds as antibacterial agents. Bacteria, protazoa and other single cell organisms have a number of deactivation pathways available which can render an amindoglycoside inactive. For example, bacteria have a number of enzymes which are capable of metabolizing an aminoglycolide into non-cytotoxic species such as by phosphorylation, saccharide bio-degradation and the like. The ability of bacterium and other single cell organisms to quickly develop resistance to aminoglycosides limits current antibiotic applications.
It would be desirable to design new aminoglycolide compounds which inhibit bacteria growth, e.g., possess anti-bacterial activity, and are not susceptible to formation of resistant cellular strains.